Seems short sided even from a bottom line perspective. For one, CERN is bound to employ plenty of experts that will familiarize themselves with the product and move on to other projects later and choose MSFT products. Additionally, CERN is such a high profile project that simply asking them to advertise the fact that they are "powered by Microsoft" would pay them more than any licensing fees.
But maybe they thought they could charge 10x the fees AND still get all the benefits.
I guess "powered by Microsoft" is not what was happening at CERN as nearly all data analysis is "powered by Linux" (there's a reason, Scientific Linux existed) and iirc the ecad-software KiCAD is the only production focused CAD-tool which is good and free (mostly sponsored by CERN too)
But maybe they thought they could charge 10x the fees AND still get all the benefits.